To delete an atom or a bond click the Erase button on the General toolbar then click on the atom or bond, or by dragging you can select the contents of a rectangle.
To delete the contents of a rectangle click on the Erase button and by dragging select what you want to delete.
You can delete a previously selected area by clicking on the Erase button or by pressing the Delete key.
You can reach the Delete function from the contextual menu or the Edit menu.